Edit:
Alright I figured out a workaround. I was trying to guess which portions of code to delete in the mod_comments.class.php by trial and error but nothing seemed to work. Instead I added a new line to manipulate the $link string.
Original code:
$link = $comObject->linkToContent($post->_item['contentid'], $post->_item['id'], true);
Code with new line added:
$link = $comObject->linkToContent($post->_item['contentid'], $post->_item['id'], true);
$link = str_ireplace("Itemid=1","",$link);
Just to clarify, links from the module used to look like this by default:
http://www.MYSITE.com/joomla/index.php?option=com_content&view=article&id=103&joscclean=1&comment_id=37&Itemid=1#josc37
Now they look like this:
http://www.MYSITE.com/joomla/index.php?option=com_content&view=article&id=103&joscclean=1&comment_id=37josc37
I hope this helps someone else in the future.